scholarly journals Molecular characterization of novel germline deletions affecting SDHD and SDHC in pheochromocytoma and paraganglioma patients

2009 ◽  
Vol 16 (3) ◽  
pp. 929-937 ◽  
Author(s):  
Jean-Pierre Bayley ◽  
Marjan M Weiss ◽  
Anneliese Grimbergen ◽  
Bernadette T J van Brussel ◽  
Frederik J Hes ◽  
...  
Keyword(s):  
Nonsense Mutations ◽  
Gene Deletions ◽  
Exon 2 ◽  
Gene Insertion ◽  
Large Deletions ◽  
Exon 1 ◽  
Long Range Pcr ◽  
Intron 2 ◽  
Dependent Probe

A major cause of paraganglioma and pheochromocytoma is germline mutation of the tumor suppressor genes SDHB, SDHC, and SDHD, encoding subunits of succinate dehydrogenase (SDH). While many SDH missense/nonsense mutations have been identified, few large deletions have been described. We performed multiplex ligation-dependent probe amplification deletion analysis in 126 point mutation-negative patients, and here we describe four novel deletions of SDHD and SDHC. Long-range PCR was used for the fine mapping of deletions. One patient had a 10 kb AluSg–AluSx-mediated deletion including SDHD exons 1 and 2, the entire TIMM8B gene, and deletion of exons of C11orf57. A second patient had a deletion of SDHD exons 1 and 2 and exon 1 of the TIMM8B gene. A third patient showed a deletion of exon 2 of SDHD, together with a 235 bp MIRb–Tensin gene insertion. In a fourth patient, a deletion of exons 5 and 6 of the SDHC gene was found, only the second SDHC deletion currently known. The deletions of the TIMM8B and C11orf57 genes are the first to be described, but do not appear to result in an additional phenotype in these patients. Four of the eight breakpoints occurred in Alu sequences and all three SDHD deletions showed an intron 2 breakpoint. This study underlines the fact that clinically relevant deletions may encompass neighboring genes, with the potential to modify phenotype. Gene deletions of SDHD and SDHC represent a substantial proportion of all mutations, and must be considered in paraganglioma patients shown to be negative for mutations by sequencing.

scholarly journals Deletion of Exon 1 in AMER1 in Osteopathia Striata with Cranial Sclerosis

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1439
Author(s):  
Jingyi Mi ◽  
Padmini Parthasarathy ◽  
Benjamin J. Halliday ◽  
Tim Morgan ◽  
John Dean ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Severe Phenotype ◽  
Gene Deletions ◽  
Exon 2 ◽  
Pathogenic Variants ◽  
Osteopathia Striata ◽  
Cranial Sclerosis ◽  
Exon 1 ◽  
Dominant Condition ◽  
Dependent Probe

Osteopathia striata with cranial sclerosis (OSCS) is an X-linked dominant condition characterised by metaphyseal striations, macrocephaly, cleft palate, and developmental delay in affected females. Males have a more severe phenotype with multi-organ malformations, and rarely survive. To date, only frameshift and nonsense variants in exon 2, the single coding exon of AMER1, or whole gene deletions have been reported to cause OSCS. In this study, we describe two families with phenotypic features typical of OSCS. Exome sequencing and multiplex ligation-dependent probe amplification (MLPA) did not identify pathogenic variants in AMER1. Therefore, genome sequencing was employed which identified two deletions containing the non-coding exon 1 of AMER1 in the families. These families highlight the importance of considering variants or deletions of upstream non-coding exons in conditions such as OSCS, noting that often such exons are not captured on probe or enrichment-based platforms because of their high G/C content.

Characterization of Partial Gene Deletions in Type III von Willebrand Disease with Alloantibody Inhibitors

1994 ◽  
Vol 72 (02) ◽  
pp. 180-185 ◽  
Author(s):  
David J Mancuso ◽  
Elodee A Tuley ◽  
Ricardo Castillo ◽  
Norma de Bosch ◽  
Pler M Mannucci ◽  
...  
Keyword(s):  
Von Willebrand Factor ◽  
Von Willebrand Disease ◽  
Pcr Analysis ◽  
Gene Deletions ◽  
Factor Gene ◽  
Type Iii ◽  
Large Deletions ◽  
Von Willebrand ◽  
Willebrand Factor

Summaryvon Willebrand factor gene deletions were characterized in four patients with severe type III von Willebrand disease and alloantibodies to von Willebrand factor. A PCR-based strategy was used to characterize the boundaries of the deletions. Identical 30 kb von Willebrand factor gene deletions which include exons 33 through 38 were identified in two siblings of one family by this method. A small 5 base pair insertion (CCTGG) was sequenced at the deletion breakpoint. PCR analysis was used to detect the deletion in three generations of the family, including two family members who are heterozygous for the deletion. In a second family, two type III vWD patients, who are distant cousins, share an -56 kb deletion of exons 22 through 43. The identification and characterization of large vWF gene deletions in these type III vWD patients provides further support for the association between large deletions in both von Willebrand factor alleles and the development of inhibitory alloantibodies.

The mouse carbonic anhydrase I gene contains two tissue-specific promoters

1989 ◽  
Vol 9 (8) ◽  
pp. 3308-3313
Author(s):  
P Fraser ◽  
P Cummings ◽  
P Curtis
Keyword(s):  
Carbonic Anhydrase ◽  
Splice Acceptor Site ◽  
Acceptor Site ◽  
Exon 2 ◽  
Tissue Specific ◽  
Isolation And Characterization ◽  
Carbonic Anhydrase I ◽  
Erythroleukemia Cells ◽  
Exon 1

We report the isolation and characterization of the mouse carbonic anhydrase I (CAI) gene. Direct RNA sequence analysis of the 5' nontranslated regions of CAI mRNA from mouse colon and mouse erythroleukemia cells demonstrated tissue specificity in the lengths and sequences of CAI transcripts. Analysis of several mouse CAI genomic clones showed that the transcripts arose from a single CAI gene with two tissue-specific promoters and eight exons. CAI transcripts in the colon were found to initiate just upstream of the erythroid exon 2 of the CAI gene region sequence. Erythroid transcripts originated from a novel promoter upstream of exon 1, which was located more than 10 but less than 250 kilobases upstream of exon 2. Erythroid exon 1 contained only a nontranslated sequence, which was spliced to exon 2 via a cryptic splice acceptor site located in the region that encoded the colon mRNA 5' nontranslated sequence. The remaining exon-intron junctions were conserved in comparison with those of the CAII and CAIII genes.

Characterization of NRG1 gene fusion events in solid tumors.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 3113-3113
Author(s):  
Sushma Jonna ◽  
Rebecca Feldman ◽  
Sai-Hong Ignatius Ou ◽  
Misako Nagasaka ◽  
Jeffrey Swensen ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Fusion Partner ◽  
Exon 2 ◽  
Downstream Signaling ◽  
Chimeric Transcripts ◽  
Exon 1 ◽  
Tumor Types ◽  
Fusion Products ◽  
Ig Domain

3113 Background: NRG1 fusions are actionable genomic alterations detected across tumor types. The NRG1 gene encode for neuregulin, which serves as a ligand for ERBB3 and ERBB4 receptors and activates downstream signaling through the MAPK and PI3K pathways. Here, we update the detection of NRG1 gene fusions across tumor types and further describe fusion characteristics. Methods: Samples submitted for clinical molecular profiling that included RNA-sequencing (Archer Dx or Caris MI transcriptome) were retrospectively analyzed for NRG1 fusion events. All NRG1 fusions with ≥ 3 junction reads were identified for manual review and for characterization of fusion class, intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations by NGS. Results: A total of 82 NRG1 fusion events (0.2% of 44,570) were identified. Among the fusions identified, the distribution across tumor types was as follows: non-small cell lung cancer (NSCLC, 54%), breast cancer (11%), ovarian cancer (7%), pancreatic cancer (7%), cholangiocarcinoma (6%), colorectal cancer (5%), and other (10%). Forty-two unique fusion partners were identified, the most common being CD74 (23%), ATP1B1 (9%), SLC3A2 (7%), RBPMS (6%) and SDC4 (4%). Almost half (47%) of all fusion events are expected to include the transmembrane domain contributed by the NRG1 fusion partner. Lung and pancreatobilliary cancers had the highest rates of transmembrane domain retention from their fusion partners (63.6% and 54.5%, respectively). In all other tumor groups, most fusion partners lacked transmembrane domains. In 15% of cases, the chimeric transcripts are predicted to lead to increased expression of NRG1. The most commonly reported breakpoints in NRG1 occur in exon 6 and exon 2. While fusions with the NRG1 breakpoint at exon 2 retain the immunoglobulin (Ig) domain and all downstream portions (including EGF-like domain), those at exon 6 do not contain the Ig portion and result in shorter chimeric proteins. The breakpoints in all CD74:NRG1 fusions, the most common fusions in NSCLC, occur at exon 5 or 6 and cause truncation of domains upstream of the EGF-like domain. In ATP1B1:NRG1 fusions, the most common fusions in pancreatobilliary cancers, the breakpoints are at exon 1 or 2 and retain the Ig domain. Conclusions: NRG1 fusion products are diverse across tumor types, but the significance of these variations is not clear. The biological and clinical implications of retaining certain domains of NRG1 (such as the Ig domain) and of fusion partners warrants further investigation.

Characterization of Exon 2 and Intron 2 of Leptin Gene in Indian Goats

2009 ◽  
Vol 20 (2) ◽  
pp. 80-85 ◽  
Author(s):  
S. K. Singh ◽  
P. K. Rout ◽  
R. Agarwal ◽  
A. Mandal ◽  
S. K. Singh ◽  
...  
Keyword(s):  
Exon 2 ◽  
Intron 2

scholarly journals Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance.

1994 ◽  
Vol 14 (9) ◽  
pp. 6317-6325 ◽  
Author(s):  
J Cheng ◽  
P Belgrader ◽  
X Zhou ◽  
L E Maquat
Keyword(s):  
Translation Initiation ◽  
Triosephosphate Isomerase ◽  
Splice Sites ◽  
Nonsense Mutations ◽  
Nonsense Codon ◽  
Exon 1 ◽  
Nonsense Codons ◽  
Intron 2 ◽  
Mediated Reduction ◽  
Downstream Movement

The translation of human triosephosphate isomerase (TPI) mRNA normally terminates at codon 249 within exon 7, the final exon. Frameshift and nonsense mutations of the type that cause translation to terminate prematurely at or upstream of codon 189 within exon 6 reduce the level of nuclear TPI mRNA to 20 to 30% of normal by a mechanism that is not a function of the distance of the nonsense codon from either the translation initiation or termination codon. In contrast, frameshift and nonsense mutations of another type that cause translation to terminate prematurely at or downstream of codon 208, also within exon 6, have no effect on the level of nuclear TPI mRNA. In this work, quantitations of RNA that derived from TPI alleles in which nonsense codons had been generated between codons 189 and 208 revealed that the boundary between the two types of nonsense codons resides between codons 192 and 195. The analysis of TPI gene insertions and deletions indicated that the positional feature differentiating the two types of nonsense codons is the distance of the nonsense codon upstream of intron 6. For example, the movement of intron 6 to a position downstream of its normal location resulted in a concomitant downstream movement of the boundary between the two types of nonsense codons. The analysis of intron 6 mutations indicated that the intron 6 effect is stipulated by the 88 nucleotides residing between the 5' and 3' splice sites. Since the deletion of intron 6 resulted in only partial abrogation of the nonsense codon-mediated reduction in the level of TPI mRNA, other sequences within TPI pre-mRNA must function in the effect. One of these sequences may be intron 2, since the deletion of intron 2 also resulted in partial abrogation of the effect. In experiments that switched introns 2 and 6, the replacement of intron 6 with intron 2 was of no consequence to the effect of a nonsense codon within either exon 1 or exon 6. In contrast, the replacement of intron 2 with intron 6 was inconsequential to the effect of a nonsense codon in exon 6 but resulted in partial abrogation of a nonsense codon in exon 1.

Identification of Three Novel Substitutions in the Erythroid Promoter of the HMBS Gene: A New Erythroid Variant of Human Acute Intermittent Porphyria?

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4574-4574
Author(s):  
Elena Di Pierro ◽  
Valeria Besana ◽  
Valentina Brancaleoni ◽  
Dario Tavazzi ◽  
Maria Domenica Cappellini
Keyword(s):  
Acute Intermittent Porphyria ◽  
Normal Subjects ◽  
Normal Function ◽  
Inherited Disorders ◽  
Exon 2 ◽  
Molecular Defects ◽  
Exon 1 ◽  
Classic Form ◽  
Partial Deficiency ◽  
Intron 2

Abstract Porphyrias are inherited disorders in the biosynthesis of heme. Acute intermittent porphyria (AIP), the most common form, is autosomal dominant and it is characterized by recurrent attacks of abdominal pain, gastrointestinal dysfunction, and neurologic disturbances. AIP is caused by molecular defects in the hydroxymethylbilane synthase gene (HMBS) causing a partial deficiency of the third enzyme of the heme biosynthetic pathway. This gene maps to chromosome 11q23.2 with a total of 15 exons. Two distinct promoters direct the synthesis of housekeeping and erythroid specific mRNAs by alternative splicing. The housekeeping promoter is located upstream the exon 1 while the erythroid promoter include a portion of intron 1, the exon 2 and the intron 2. The exon 1 and the exons 3 to 15 generate the housekeeping mRNA while the exons 2 to 15 generate the erythroid mRNA giving rise to the housekeeping HMBS isoform and to the erythroid HMBS isoform respectively. In the classic form of AIP, both the housekeeping and the erythroid HMBS isoforms are deficient since the must common molecular defects involve the common region of the gene from exon 3 to exon 15. Approximately 5% of AIP patients have normal levels of the erythroid HMBS isoform and defects in the housekeeping promoter or in the exon 1 which is specific for the housekeeping HMBS isoform, causing the ‘non-erythroid variant’ of AIP. So far no mutations are known in the erythroid promoter. In this study we searched for molecular defects in HMBS gene in three Italian patients with typical clinical and biochemical signs of AIP. The diagnosis was based on elevated urinary excretion of porphyrinic precursors and reduced erythrocyte HMBS activity. The entire HMBS gene has been amplified by PCR and submitted to direct automated sequencing: no mutations known as responsible for classic form of AIP have been identified. However, each of three patients had a substitutions in the erythroid promoter of HMBS gene that could justify the reduced erythrocyte HMBS activity: c.34–115 C>A, c.34–126 G>C and c.34–156G>A. In order to establish if these substitutions were polymorphisms, more than 200 alleles from Italian normal subjects were sequenced and none of them revealed the substitutions. These three mutations, located specifically in the intron 2, could affect the normal splicing of exon 3 causing an abnormal mRNA, to give rise to the classical form of AIP. The mRNA analysis, however, didn’t reveal any abnormal mRNA. Moreover real time experiments in the lymphocytes showed a 100% expression of housekeeping HMBS mRNA excluding the non-sense mediated decay mechanism. These data suggest that these mutations could affect the normal function of the erythroid promoter only, causing an erythroid variant of human acute intermittent porphyria. Further expression studies are in progress.

Mutational screening of six afibrinogenemic patients: Identification and characterization of four novel molecular defects

2007 ◽  
Vol 97 (04) ◽  
pp. 546-551 ◽  
Author(s):  
Luca Monaldini ◽  
Rosanna Asselta ◽  
Stefano Duga ◽  
Flora Peyvandi ◽  
Mehran Karimi ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Point Mutations ◽  
Large Deletion ◽  
Genetic Defects ◽  
Coagulation Disorder ◽  
Recessive Trait ◽  
Large Deletions ◽  
Exon 1 ◽  
Congenital Afibrinogenemia

SummaryCongenital afibrinogenemia (CAF) is a rare coagulation disorder characterized by very low or unmeasurable levels of functional and immunoreactive fibrinogen in plasma, associated with a hemorrhagic phenotype of variable severity. It is transmitted as an autosomal recessive trait (prevalence 1:1,000,000) and is invariantly associated with mutations affecting one of the three fibrinogen genes (FGA, FGB, and FGG, coding for Aα, Bβ, and γ chain, respectively). Fibrinogen is secreted by hepatocytes as a hexamer composed of two copies of each chain; the lack of one chain has been demonstrated to prevent its secretion. Most genetic defects causing afibrinogenemia are point mutations, where- as only three large deletions have been identified so far, all affecting the FGA gene. We here report the molecular characterization of six unrelated afibrinogenemic patients leading to the identification of eight different mutations, four hitherto unknown: a 4.1-Kb large deletion involving exon 1 of FGA (AC107385:g. 65682_69828del), two nonsense mutations (p.Trp229X in FGA and p.Trp266X in FGB), and an ins-del mutation (g.1787_ 1789del3ins12) in FGA. The molecular characterization of CAFcausing genetic defects increases our understanding on the genetic basis of this disease and might be helpful for prenatal screening purposes, as also demonstrated during this study.

scholarly journals Molecular characterization of erythrocyte glycophorin C variants

Blood ◽  
1991 ◽  
Vol 77 (3) ◽  
pp. 644-648
Author(s):  
S Chang ◽  
ME Reid ◽  
J Conboy ◽  
YW Kan ◽  
N Mohandas
Keyword(s):  
Molecular Characterization ◽  
Mechanical Stability ◽  
Exon 2 ◽  
Mrna Sequencing ◽  
Erythrocyte Shape ◽  
Altered Glycosylation ◽  
Exon 1 ◽  
Dna Fragment ◽  
Glycophorin C

Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA. Sequencing of the mutant 338-bp fragment identified a 57-bp deletion that corresponds to exon 2 of the glycophorin C gene. Similar analysis showed deletion of 84-bp exon 3 in the Gerbich phenotype. In contrast to the generation of shorter than normal DNA fragments from mRNA amplification in the Yus and Gerbich phenotypes, amplification of mRNA from the Webb phenotype generated a normal-sized fragment. Sequencing of this DNA fragment showed an A----G substitution at nucleotide 23 of the coding sequence, resulting in the substitution of asparagine by serine. This modification accounts for the altered glycosylation of glycophorin C seen in this phenotype. These results have enabled us to characterize glycophorin C variants in three different phenotypes that involve deletions of exons 2 and 3 of the glycophorin C gene, as well as a point mutation in exon 1 that results in altered glycosylation of this protein.

A 20.7 kb Deletion within the Factor VIII Gene Associated with LINE-1 Element Insertion

1998 ◽  
Vol 79 (05) ◽  
pp. 938-942 ◽  
Author(s):  
Neil Van de Water ◽  
Ruth Williams ◽  
Paul Ockelford ◽  
Peter Browett
Keyword(s):  
Factor Viii ◽  
Molecular Mechanisms ◽  
Haemophilia A ◽  
Factor Viii Gene ◽  
Normal Sequence ◽  
Large Deletions ◽  
Flanking Region ◽  
Long Range Pcr ◽  
L1 Element

SummaryLarge deletions within the factor VIII gene account for approximately 5% of the mutations causing haemophilia A. The characterization of such mutations can provide insights into the molecular mechanisms of these and other deletions in man. We have analyzed a 20.7 kb deletion spanning exons 15 to 20 within the factor VIII gene in a patient with severe haemophilia A. Long range PCR was used to investigate the extent of the deletion and to provide a template for sequencing across the deletion breakpoint. A 38-base insertion homologous to the 3’ region of a LINE-1 (L1) element was detected at the breakpoint of the deletion. Normal sequence at the 5’ breakpoint in intron 14 was homologous to an L1 flanking region and normal sequence at the 3’ breakpoint in intron 20 was homologous to an adjacent sequence within the same L1 flanking region. A molecular mechanism for the deletion involving retrotransposition of a readthrough product of an L1 element plus its 3’ flanking region is suggested.

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